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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttttcttatctgtgatgacatgttattgaatctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA

Basic information

species Vitis vinifera
transcript Vv11s0052g01380.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttttcttatctgtgatgacatgttattgaatctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
               ||| | |  |||| | ||    || | | | ||||   | ||||| |       | ||     | ||  |    |   ||     |||||||| ||||||||||| || |||||  |||  |||||||| |||||||||||||||||||| ||||||||| |||| ||||||| ||||||         
--------gtatgattccatatactttactgatc---ttgtgtaactgttacatgtcttaac-------atatagatcttaaattataatccctctt---gtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 5
gtaggttcaggctcatccttgtcttttatttattgaattattt-tattgttctttttcttatctgtgatgacatgttattgaatctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
              ||  ||| |  | | ||||||  ||| |  || || |   |   ||   ||| |   |  ||||   |   | || || |  | ||   |||||| || || ||||||||||||||  |||  |||||||| |||||||| || |||||||||||||||||| |||||||||||| | |||||        
------------gtatgtttg-caatgagttattgttttactcatactgctagatgatttgaatgtta---ctcgttaaccatatttctattgtatcttg--cagTGTACAAAAAGCACTATCCACCTGCCCTAAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGTGCATTCCACAAGAAGTTAAATGCAAGTGG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AC202073.4_FGT001 (Zea mays), 3'ss of exon 4
gtaggttcaggctcatccttgtct-tttatttattgaattattttattgttctttttcttatctgtgatgacatgttattgaatctgctg-tttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
                    || | |||||||| ||  | || | ||||||   |    || |    | |   |     |||||  | |   |    | |  |||||||||||||| || ||||| |||||| |||  ||||| || |||||||| || |||||||| |||||||||||||||||||||||  ||||         
--------------------gtatgtttatttagtg--tgatgtcattgttaaataatctaacatataggctttaaacatgaatacgttaactaactcttttgtagTGTATAAGAAGCATTATCCTCCTGCACTAAAGGATGAGGTATGGAGATTAGAAAAGATTGGAAAGGATGGTTCATTCCACAAGAGATTAAACTCAAGTGG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 5
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttttcttatctgtgatgacatgttattgaatctgctg-tttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
||| ||   | | ||   |||   |||| | |||  || |    |   ||   | | || |  |   |  |||       |   ||||| ||||    |   ||||||| ||||| ||||| ||||||||  | |  |||||||| |||||||| || |||||||||||||||||  |||||||||||| | |||||        
gtatgtgt-gacacactgttga--tttactcattagatgaaacaaagattacctgtatttttagaatttgcat--cgccaagcatgctgattttgtatttattagTGTACAAGAAGCACTACCCACCTGCGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCCAGTGG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 5
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttttcttatctgtga-tgacat-gttattgaatctgctg-tttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
||| ||   |   |||  |||   |||| | |||  || ||   |   ||   | | || | |   | |  |||   |    |   ||||| || |    |   ||||||| || |||||||| |||||  |  | |  |||||||| |||||||| || |||||||||||||||||  |||||||||||| | |||||  |     
gtatgtgt-gatacattgttga--tttactcattagatgatacaaagattacgtgtattttttagaacttgcatcagttgcaagcatgctgattctgtatttattagTGTACAAAAAACACTACCCACCCACGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCTAGTGG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttttcttatctgtgatgacatgttattgaa-tctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
                         | | |     || | | |   ||| || | |     ||    |||||| |   | || | |     |||    |   ||||||| ||||| |||||||||||| || | |  ||||| || ||||| ||||| || || || |||||||| |||||||| |||||||| || || ||   
------------------------gtaagtcccaaaaatgtatctgtgtactgtattcccact----tgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G010471_T01 (Zea mays), 3'ss of exon 1
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttttcttatctgtgatgacatgttattgaa-tctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
                         | | |     || | | ||  ||| || | |  |  ||    |||||| |   | || | |     |||    |   ||||||| ||||| |||||||||||| || | |  ||||| || ||||| ||||| || || || |||||||| |||||||| |||||||| || || ||   
------------------------gtaagtcccaaaaatgtatttgtgtgctgtattctcact----tgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 5
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttttcttatctgtgatgacatgttattgaa-tctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
                                  | |       |    |  ||||  ||| | |  |||||  |   | || | | |    ||    |   ||||||| ||||| |||||||||||| |  |||  ||||| || ||||| ||||| || || || |||||||| |||||||| |||||||| || || ||   
----------------------------------gtaagtcccaaaaaattgtttttgtatttctattgacacatatctaaactattccagattcatttacctagTGTACAAGAAGCACTATCCACCTACGCTAAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGAAAGGATGGCTCATTCCATAAGAGGCTGAACAAATCTGG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttt----tcttatctgtgatgacatgttattgaatctgctgtttttccctgggt---agTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
|||||   | |||  ||    ||||||| || ||   |    | | |  |||       |||   || | ||  ||| || || ||| |  | ||||  |||   |   ||| |||||||| || |||||||| ||||| |||||||| |||||||||||||||||||| ||||||||||| |||||||| |||| ||| |||||| |   
gtagggctatgct--tctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatctt-ttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 6
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttcttttt---cttat-ctgtgatgacatgttattgaatctgctgtttttccctgggt---agTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
||||| | | |||  ||    ||||||| || ||   |    | | || |||   |   | ||  |||| ||  ||| || || ||| |  | ||||  |||   |   ||| |||||||| || |||||||||||||| |||||||| |||||||||||||||||||| ||||||||||| ||||| || |||| ||| |||| | |   
gtagggttatgct--tctacatcttttagtttttctctagcatcagtgctctccctgctcctacactgtaatagcatctt-ttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCTGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTTCATAAGAAGCTGAATAGTGCAGG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttttcttatctgtgatgacatgttattgaatctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
||| | ||         |   | || |  | | || |  || |  |  ||  || | |||  | ||||| ||  ||              | ||   || | |||||| ||||| || |||||||||||  | | ||||||||||||||||||||| ||||| |||||||||||  ||||||| || | ||| | |  |     
gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtt-tgatg-cacatt--------------tcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG

upper sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaggttcaggctcatccttgtcttttatttattgaattat-tttattgttctttttcttatctgtgatgacatgttattgaatctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
    ||    | |     || |  ||   || |||  || |  ||     |  |||||||  ||      ||||||| ||| ||  | | | |        |||||||| ||||| || ||||||||||| || | |||||| |||||||| || ||||||||||| || |||||  | || || ||||||||||    | |   
----gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttctt--ctaaatcaacatgttgttggattggttatgt--------gtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110719043|gb|EE096564.1|EE096564
EST:     ACGTGAAGCCAAAACAGAAGCTTTCACTGTTAAAGATCACAGGGGGGAAT                         TGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGG
genomic: ACGTGAAGCCAAAACAGAAGCTTTCACTGTTAAAGATCACAGGGGGGAATgtaggttcag ... ccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttttcttatctgtgatgacatgttattgaatctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
                                 tctgctgtttttccct  CT-rich tract
                         ttattgaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttttcttatctgtgatgacatgttattgaatctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG